Exploring the polyurethanolytic activity and microbial composition of landfill microbial communities.

The microbial composition of polyurethane degrading communities has been barely addressed, and it is unknown if microenvironmental conditions modify its composition, affecting its biodegradative capacity. The polyurethanolytic activity and taxonomic composition of five microbial communities, selected by enrichment in the polyether-polyurethane-acrylic (PE-PU-A) coating PolyLack®, from deteriorated PU foams collected at different microenvironments in a municipal landfill (El Bordo Poniente, BP) were explored. All BP communities grew similarly in PolyLack® as the sole carbon source, although BP1, BP4, and BP5 showed better performance than BP2 and BP7. FTIR spectroscopy showed that ester, urethane, ether, aromatic and aliphatic groups, and the acrylate component were targets of the biodegradative activity. Extracellular esterase activity was higher at 5 days of cultivation and decreased at 21 days, while urease activity showed the opposite. Microbial composition analysis, assessed by 16S rDNA V3 region PCR-DGGE, revealed a preponderance of Rhizobiales and Micrococcales. The reported PU-degrading genera Paracoccus, Acinetobacter, and Pseudomonas were identified. In contrast, Advenella, Bordetella, Microbacterium, Castellaniella, and Populibacterium, some of them xenobiotics degraders, can be considered potentially PU-degrading genera. Correspondence analysis identified independent groups for all communities, except the BP4 and BP5. Although partial taxonomic redundancy was detected, unique OTUs were identified, e.g., three members of the Weeksellaceae family were present only in the BP4/BP5 group. These results suggest that the microenvironmental conditions where the landfill microbial communities were collected shaped their taxonomical composition, impacting their PE-PU biodegradative capacities. These BP communities represent valuable biological material for the treatment of PU waste and other xenobiotics. KEY POINTS: • Landfill microbial communities display slightly different capacities for growing in polyether-polyurethane-acrylic. • Ester, urethane, ether, aromatic, aliphatic, and acrylate groups were attacked. • Esterase activity was more significant at early culture times while urease activity at latter. • Landfill microenvironments shape partial taxonomical redundancy in the communities. • Best communities' performance seems to be related to unique members' composition.

Genomic and functional characterisation of two Enterococcus strains isolated from Cotija cheese and their potential role in ripening.

Enterococcus spp. are present in the native microbiota of many traditional fermented foods. Their ability to produce antibacterial compounds, mainly against Listeria monocytogenes, has raised interest recently. However, there is scarce information about their proteolytic and lipolytic potential, and their biotechnological application is currently limited because enterococcal strains have been related to nosocomial infections. In this work, next-generation sequencing and optimised bioinformatic pipelines were used to annotate the genomes of two Enterococcus strains-one E. faecium and one E. faecalis-isolated from the Mexican artisanal ripened Cotija cheese. A battery of genes involved in their proteolytic system was annotated. Genes coding for lipases, esterases and other enzymes whose final products contribute to cheese aroma and flavour were identified as well. As for the production of antibacterial compounds, several peptidoglycan hydrolase- and bacteriocin-coding genes were identified in both genomes experimentally and by bioinformatic analyses. E. faecalis showed resistance to aminoglycosides and E. faecium to aminoglycosides and macrolides, as predicted by the genome functional annotation. No pathogenicity islands were found in any of the strains, although traits such as the ability of biofilm formation and cell aggregation were observed. Finally, a comparative genomic analysis was able to discriminate between the food strains isolated and nosocomial strains. In summary, pathogenic strains are resistant to a wide range of antibiotics and contain virulence factors that cause host damage; in contrast, food strains display less antibiotic resistance, include genes that encode class II bacteriocins and express virulence factors associated with host colonisation rather than invasion.

Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota.

Cotija cheese is a Mexican handcrafted product made from raw cow milk whose ripening process occurs spontaneously and, presumably, it is influenced by environmental conditions. Its sensory characteristics and safety are probably the result of the balance between microbial populations and their metabolic capacity. In this work, we studied the dominance and richness of the bacteria in the Cotija cheese microbiome, as well as their metabolic potential by high-throughput sequencing. By the analysis of 16S ribosomal sequences, it was found that this metagenome is composed mainly of three dominant genera: Lactobacillus, Leuconostoc and Weissella, and more than 500 of non-dominant genera grouped in 31 phyla of both bacteria and archaea. The analysis of single-copy marker genes reported a similar result for dominant genera, although with greater resolution that reached the species level. Pathogenic bacteria such as Salmonella, Listeria monocytogenes, Brucella or Mycobacterium were not found. The Cotija cheese microbiome has the metabolic capacity for the synthesis of a wide range of flavor compounds, mainly involved with the metabolism of branched chain amino acids and free fatty acids. Genes associated with bacteriocin production and immunity were also found. Arguably, this is one of the most diverse metagenomes among the microbial communities related to fermented products.